Evaluation of gene prediction software using a genomic data set: application to <$O_SSF>Arabidopsis thaliana<$C_SSF>sequences. - Nathalie Pavy; Stephane Rombauts; Patrice Déhais; Catherine Mathé; Ramana V. Davuluri; Philippe Leroy; Pierre Rouzé (Bioinform., 1999)

Identifying the 3'-terminal exon in human DNA. - Jack E. Tabaska; Ramana V. Davuluri; Michael Q. Zhang (Bioinform., 2001)

AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. - Ramana V. Davuluri; Hao Sun 001; Saranyan K. Palaniswamy; Nicole Matthews; Carlos Molina; Mike Kurtz; Erich Grotewold (BMC Bioinform., 2003)

Java-based application framework for visualization of gene regulatory region annotations. - Hao Sun 001; Ramana V. Davuluri (Bioinform., 2004)

HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development. - Twyla T. Pohar; Hao Sun 001; Ramana V. Davuluri (Nucleic Acids Res., 2004)

OMGProm: a database of orthologous mammalian gene promoters. - Saranyan K. Palaniswamy; Victor X. Jin; Hao Sun 001; Ramana V. Davuluri (Bioinform., 2005)

A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha. - Lang Li 001; Alfred S. L. Cheng; Victor X. Jin; Henry H. Paik; Meiyun Fan; Xiaoman Li; Wei Zhang; Jason Robarge; Curtis Balch; Ramana V. Davuluri; Sun Kim; Tim Hui-Ming Huang; et al. (Bioinform., 2006)

Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs. - Victor X. Jin; Gregory A. Singer; Francisco J. Agosto-Perez; Sandya Liyanarachchi; Ramana V. Davuluri (BMC Bioinform., 2006)

MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. - Hao Sun 001; Saranyan K. Palaniswamy; Twyla T. Pohar; Victor X. Jin; Tim Hui-Ming Huang; Ramana V. Davuluri (Nucleic Acids Res., 2006)

An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules. - Huaxia Qin; Michael W. Y. Chan; Sandya Liyanarachchi; Curtis Balch; Dustin P. Potter; Irene J. Souriraj; Alfred S. L. Cheng; Francisco J. Agosto-Perez; Elena Nikonova; Pearlly Yan; Huey-Jen Lin; Kenneth P. Nephew; et al. (BMC Syst. Biol., 2009)

Data mining of mRNA-Seq and small RNA-Seq data to find microRNA targets. - Hyunsoo Kim; Ramana V. Davuluri (BCB, 2010)

Estimating the Expression of Transcript Isoforms from mRNA-Seq via Nonnegative Least Squares. - Hyunsoo Kim; Yingtao Bi; Ramana V. Davuluri (BIBE, 2010)

Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data. - Ravi Gupta; Priyankara Wikramasinghe; Anirban Bhattacharyya; Francisco A. Perez; Sharmistha Pal; Ramana V. Davuluri (BMC Bioinform., 2010)

IsoformEx: Isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data. - Hyunsoo Kim; Yingtao Bi; Sharmistha Pal; Ravi Gupta; Ramana V. Davuluri (BMC Bioinform., 2011)

MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data. - Ravi Gupta; Anirban Bhattacharyya; Francisco J. Agosto-Perez; Priyankara Wikramasinghe; Ramana V. Davuluri (Nucleic Acids Res., 2011)

Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. - Hao Sun 001; Jiejun Wu; Priyankara Wikramasinghe; Sharmistha Pal; Ravi Gupta; Anirban Bhattacharyya; Francisco J. Agosto-Perez; Louise C. Showe; Tim Hui-Ming Huang; Ramana V. Davuluri (Nucleic Acids Res., 2011)

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data. - Yingtao Bi; Ramana V. Davuluri (BMC Bioinform., 2013)

Comparison of data discretization methods for cross platform transfer of gene-expression based tumor subtyping classifier. - Segun Jung; Yingtao Bi; Ramana V. Davuluri (ICCABS, 2014)

Identification of candidate regulatory SNPs by integrative analysis for prostate cancer genome data. - Segun Jung; Hongjian Jin; Ramana V. Davuluri (BCB, 2015)

Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms. - Matthew Dapas; Manoj Kandpal; Yingtao Bi; Ramana V. Davuluri (Briefings Bioinform., 2017)

Multivariate Analysis of Preoperative Magnetic Resonance Imaging Reveals Transcriptomic Classification of de novo Glioblastoma Patients. - Saima Rathore; Hamed Akbari; Spyridon Bakas; Jared Pisapia; Gaurav Shukla; Jeffrey D. Rudie; Xiao Da; Ramana V. Davuluri; Nadia Dahmane; Donald M. O'Rourke; Christos Davatzikos (Frontiers Comput. Neurosci., 2019)

ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs. - Abhijit Chakraborty 003; Ferhat Ay; Ramana V. Davuluri (Bioinform., 2021)

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome. - Yanrong Ji; Zhihan Zhou 001; Han Liu 001; Ramana V. Davuluri (Bioinform., 2021)

DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome. - Zhihan Zhou 001; Yanrong Ji; Weijian Li 002; Pratik Dutta; Ramana V. Davuluri; Han Liu 001 (CoRR, 2023)

DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genomes. - Zhihan Zhou 001; Yanrong Ji; Weijian Li 002; Pratik Dutta; Ramana V. Davuluri; Han Liu 001 (ICLR, 2024)

DNABERT-S: Learning Species-Aware DNA Embedding with Genome Foundation Models. - Zhihan Zhou 001; Weimin Wu; Harrison Ho; Jiayi Wang; Lizhen Shi; Ramana V. Davuluri; Zhong Wang; Han Liu 001 (CoRR, 2024)